Align Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine (characterized, see rationale)
to candidate AZOBR_RS15680 AZOBR_RS15680 amino acid ABC transporter permease
Query= uniprot:Q31RN9 (396 letters) >FitnessBrowser__azobra:AZOBR_RS15680 Length = 216 Score = 128 bits (322), Expect = 1e-34 Identities = 81/219 (36%), Positives = 133/219 (60%), Gaps = 16/219 (7%) Query: 180 LRPVSSNDWSGLLL----TLATALISMVCSLPLGILLALGRQSSLPAIRWLSVTYIELFR 235 +R S N++ LL TLA + I+ + +G+++AL R S + A+R + YI+LF+ Sbjct: 1 IRAFSYNEFLFLLSAVQWTLALSAIAFIGGATVGLVIALARTSDIKAVRLAATGYIQLFQ 60 Query: 236 GLPLVT---ILFFGQVMVPLMLDSEWRIDRILRAIVGLTIFLSAYLAETVRGGLQAIPQG 292 G PL+ ++FFG ++ L L+ W A +GLT+ SA+L E RG +QA+P+G Sbjct: 61 GTPLLMQLFLVFFGATVMGLDLNP-WAA-----AALGLTLNASAFLGEIWRGCIQAVPRG 114 Query: 293 QFEAAAALGLNLFQTYRFIVLPQALRISIPAIVGLFLNLLQDTTLLSIVGLLELLGISRS 352 Q+EAA+ALGL R+++LPQA+++++P VG + L++ T+L +I+G EL + Sbjct: 115 QWEAASALGLRYPGLMRYVILPQAVKVAVPPTVGFLVQLIKSTSLAAIIGFTELTRAGQ- 173 Query: 353 ILANPAYLGRYAEVYLFLGVLYWLCCYGLAQLSRRLEQR 391 + N A + V+ + VLY+L C+ L+ LS RLE+R Sbjct: 174 -IVNNATFQPFL-VFGIVAVLYFLMCWPLSLLSARLERR 210 Lambda K H 0.329 0.142 0.471 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 211 Number of extensions: 11 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 396 Length of database: 216 Length adjustment: 26 Effective length of query: 370 Effective length of database: 190 Effective search space: 70300 Effective search space used: 70300 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory